Question: KEGGSOAP: problem with get.pathways.by.genes()
10.3 years ago by
Julien Meunier • 30
Julien Meunier • 30 wrote:
Hi everyone, I am trying to convert entrez id (mouse) to KEGG pathway using the keggsoap package, and having a hard time. get.genes.by.pathway(c("path:mmu04060")) would give me the following result:  "mmu:100044793" "mmu:100047704" "mmu:110542" "mmu:11477" "mmu:11479" ... However, the following get.pathways.by.genes(c("mmu:11479")) returns character(0) I also tested get.pathways.by.genes with the IL2 gene (entrez id 16183) involved in several pathways, calling the function with "16183", "mmu:16183" and other variations with the same result. The vignette mentioned they might be "problem on the server side" with get.pathways.by.genes(), and I googled without succes. Any ideas to get this function to work ? Thank you for your time, Julien PS: I known I can use KEGG.db or org.Mm.eg.db, or other locale packages but for some reason I would rather use an online query.
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